Ab Initio Molecular Dynamics Study Research Articles

Ab initio molecular dynamics simulations of the ferroelectric-paraelectric phase transition in sodium nitrite

This paper reports on the first ab initio molecular dynamics study of the ferroelectric sodium nitrite, shedding light on its ferroelctric-paraelectric phase transition. The remnant polarization ${P}_{r}$ was calculated using a Mulliken population analysis and maximally localized Wannier functions. Especially the Wannier based model is in outstanding agreement with experimental findings and previous Berry phase calculations. The simulations predict a ferroelectric Curie temperature ${T}_{c}$ between 425 and $450\phantom{\rule{4pt}{0ex}}\mathrm{K}$ in excellent agreement with the experimental value of $437\phantom{\rule{4pt}{0ex}}\mathrm{K}$. In addition, the anomalous lattice behavior (shrinking of the $c$ axis) during the phase transition is reproduced. Furthermore, the analysis of the phase transition revealed a combined displacive and order-disorder mechanism. The crystal field effect in the material could be quantified by investigating the molecular dipoles based on the maximally localized Wannier functions and the intermolecular charge transfer by analyzing the Mulliken charges. In agreement with earlier experimental and theoretical findings, the polarization reversal mechanism was found to be dominated by a $c$-axis rotation of the nitrite ions. The molecular insight into such a simple and prototypical material serves as a basis for a further development of more complex crystalline ferroelectrics, using a design principle inspired by ${\mathrm{NaNO}}_{2}$.

Formation of complex organic molecules in ice mantles: An ab initio molecular dynamics study

We present a detailed simulation of a dust grain covered by a decamer of (CH3OH)10-ice-mantle, bombarded by an OH− closed-shell molecule with kinetic energies from 10–22 eV. The chemical pathways are studied through Born-Oppenheimer (ab initio) molecular dynamics. The simulations show that methanol ice-mantles can be a key generator of complex organic molecules (COMs). We report the formation of COMs such as methylene glycol (CH2(OH)2) and the OCH2OH radical, which have not been detected yet in the interstellar medium (ISM). We discuss the chemical formation of new species through the reaction of CH3OH with the hydroxyl projectile. The dependence of the outcome on the kinetic energy of the projectile and the implications for the observation and detection of these molecules might explain why the methoxy radical (CH3 ⋅ ) has been observed in a wider range of astrophysical environments than the hydroxymethyl (CH2OH ⋅) isomer. Because of the projectile kinetic energies required for these reactions to occur, we suggest that these processes are likely relevant in the production of COMs in photodissociation and shock regions produced by high-velocity jets and outflows from young stellar objects.

Profound softening and shear-induced melting of diamond under extreme conditions: An ab-initio molecular dynamics study

Diamond retains original crystal form and large elastic stiffness up to very high temperatures, and strengthens considerably under high pressures. These remarkable characters dictate its behaviors under extreme loadings such as those in laser-heated diamond anvil cells (LHDACs) or giant planetary interiors. Here we report surprising findings from ab initio molecular dynamics simulations revealing that diamond's mechanical strengths reduce precipitously at elevated temperatures, by 50% at 3000 K, despite that its elastic parameters remain little changed. Our results also unravel an extraordinary shear-induced reduction of melting temperature of diamond under (111)[112¯] shear strains by as much as 1150 K, greatly altering its pressure-temperature (p−T) phase diagram when shear deformations exist. These new benchmarks offer crucial insights for elucidating extreme mechanics of diamond at high p-T conditions, advancing fundamental knowledge with major implications for LHDAC operation and planetary modeling.

Ultrafast Proton Transport between a Hydroxy Acid and a Nitrogen Base along Solvent Bridges Governed by the Hydroxide/Methoxide Transfer Mechanism.

Aqueous proton transport plays a key role in acid–base neutralization and energy transport through biological membranes and hydrogen fuel cells. Extensive experimental and theoretical studies have resulted in a highly detailed elucidation of one of the underlying microscopic mechanisms for aqueous excess proton transport, known as the von Grotthuss mechanism, involving different hydrated proton configurations with associated high fluxional structural dynamics. Hydroxide transport, with approximately 2-fold-lower bulk diffusion rates compared to those of excess protons, has received much less attention. We present femtosecond UV/IR pump–probe experiments and ab initio molecular dynamics simulations of different proton transport pathways of bifunctional photoacid 7-hydroxyquinoline (7HQ) in water/methanol mixtures. For 7HQ solvent-dependent photoacidity, free-energy–reactivity correlation behavior and quantum mechanics/molecular mechanics (QM/MM) trajectories point to a dominant OH–/CH3O– transport pathway for all water/methanol mixing ratios investigated. Our joint ultrafast infrared spectroscopic and ab initio molecular dynamics study provides conclusive evidence for the hydrolysis/methanolysis acid–base neutralization pathway, as formulated by Manfred Eigen half a century ago. Our findings on the distinctly different acid–base reactivities for aromatic hydroxyl and aromatic nitrogen functionalities suggest the usefulness of further exploration of these free-energy–reactivity correlations as a function of solvent polarity. Ultimately the determination of solvent-dependent acidities will contribute to a better understanding of proton-transport mechanisms at weakly polar surfaces and near polar or ionic regions in transmembrane proton pump proteins or hydrogen fuel cell materials.

Role of Inorganic Surface Layer on Solid Electrolyte Interphase Evolution at Li-Metal Anodes.

Lithium metal is an ideal anode for rechargeable lithium-battery technology. However, the extreme reactivity of Li metal with electrolytes leads to solid electrolyte interphase (SEI) layers that often impede Li+ transport across interfaces. The challenge is to predict the chemical, structural, and topographical heterogeneities of SEI layers arising from a multitude of interfacial constituents. Traditionally, the pathways and products of electrolyte decomposition processes were analyzed with the basic and simplifying presumption of an initial pristine Li-metal surface. However, ubiquitous inorganic passivation layers on Li metal can reduce electronic charge transfer to the electrolyte and significantly alter the SEI layer evolution. In this study, we analyzed the effect of nanometric Li2O, LiOH, and Li2CO3 as surface passivation layers on the interfacial reactivity of Li metal, using ab initio molecular dynamics (AIMD) calculations and X-ray photoelectron spectroscopy (XPS) measurements. These nanometric layers impede the electronic charge transfer to the electrolyte and thereby provide some degree of passivation (compared to pristine lithium metal) by altering the redox-based decomposition process. The Li2O, LiOH, and Li2CO3 layers admit varying levels of electron transfer from a Li-metal slab and subsequent storage of the electronic charges within their structures. As a result, their ability to transfer electrons to the electrolyte molecules, as well as the extent of decomposition of bis(trifluoromethanesulfonyl)imide anions, is significantly reduced compared to similar processes on pristine Li metal. The XPS experiments revealed that when Li2O is the major component on the altered surface, LiF phases formed to a greater extent. The presence of a dominant LiOH layer, however, results in enhanced sulfur decomposition processes. From AIMD studies, these observations can be explained based on the calculated quantities of electronic charge transfer found for each of the passivating films.

An ab initio molecular dynamics study of benzene in water at supercritical conditions: Structure, dynamics, and polarity of hydration shell water and the solute.

Anisotropic structure and dynamics of the hydration shell of a benzene solute in supercritical water are investigated by means of ab initio molecular dynamics simulations. The polarity and structural distortion of the benzene solute in supercritical water are also investigated in this study. Calculations are done at 673 K for three different densities of the solvent. The simulations are carried out using the Becke-Lee-Yang-Parr (BLYP) and also the Becke-Lee-Yang-Parr functional including dispersion corrections of Grimme (BYLP-D). The structural anisotropy is found to exist even at supercritical conditions as elucidated by the radial distribution functions of different conical regions and also by angular and spatial distribution functions. The benzene-water πH-bond and also the water-water hydrogen bonds are found to exist even at the supercritical temperature of 673 K. However, the numbers of these hydrogen bonds are reduced substantially with a decrease in water density. The water molecules in the axial region of benzene are found to be preferably oriented with one OH vector pointing toward the benzene ring, whereas the water molecules located in the equatorial region are found to orient their dipoles mostly parallel to the ring plane. The orientational distributions, however, are found to be rather broad at the supercritical temperature due to thermal fluctuations. Although the water molecules have faster dynamics at these supercritical conditions, a slight difference is observed in the dynamics of the solvation shell and bulk molecules. The conformational flexibility of the ring is found to be enhanced which causes an increase in polarity of the benzene solute in water under supercritical conditions.

Theoretical study of self-trapped hole diffusion in CaF2, SrF2, BaF2 crystals

In this paper we present the results of ab initio molecular dynamics (MD) study of the Vk-center in CaF2, SrF2, BaF2 crystals. The calculations have been carried using density functional theory in DFT + U approximation. The MD simulation showed three possible diffusion channels of Vk-center: (i) 0°-degree jump, (ii) jump with 90° reorientation, and (iii) jump through an intermediate state in BaF2 and SrF2 crystals. The intermediate state appears when one of the fluorine ions composing Vk-center is displaced into the nearest interstitial position and may be considered as the pair of nearest anion vacancy and H-center. This state cannot be considered as standalone Vk-center configuration but is rather metastable and briefly relaxes into ground state of Vk-center. The existence of this state in SrF2 and BaF2 crystals distinguish them from CaF2 crystal where it has not been observed.

Ab Initio Molecular Dynamics Study of the Interaction between Defects during Nonradiative Recombination

Herein, we apply ab initio molecular dynamics simulations based on a multireference description of the electronic structure to model the excited-state dynamics of models of the silicon (111) surfac...

Lithium diffusion in Li2X ( X=O , S, and Se): Ab initio simulations and inelastic neutron scattering measurements

We have performed ab-initio lattice dynamics and molecular dynamics studies of Li2X (X=O, S and Se) to understand the ionic conduction in these compounds. The inelastic neutron scattering measurements on Li2O have been performed across its superionic transition temperature of about 1200 K. The experimental spectra show significant changes around the superionic transition temperature, which is attributed to large diffusion of lithium as well as its large vibrational amplitude. We have identified a correlation between the chemical pressure (ionic radius of X atom) and the superionic transition temperature. The simulations are able to provide the ionic diffusion pathways in Li2X.

Asymmetrical vibrational energy propagation through double or single bonds of small organic molecules. An ab-initio molecular dynamics study

The present study evaluates the vibrational energy propagation from an OC stretching through the double or single bonds of two small carboxamide molecules. The results show that double bonding facilitates vibrational energy flow while single bonding blockades energy protrusion. Similarly, the direct injection of vibrational energy at a single bond precludes the dissipation of vibrational energy to the rest of the molecular structure generating a vibrational trapping effect. Correlation between bond oscillations and molecular orbital energy fluctuation are analyzed. The presence or absence of those correlations seems to be determinant for vibrational energy flow at the molecular scale.

(Invited) Discovering Design Principles for Anion Exchange Membranes with High Hydroxide Conductivity: An Ab Initio Molecular Dynamics Study

It is clear that in the identification and development of clean energy sources, a range of technologies will need to be leveraged. Electrochemical devices are an important part of this mix of technologies, and among these, fuel cells constitute some of the cleanest and most sustainable. However, several key hurdles to harnessing the potential of fuel cells (as well as various other electrochemical technologies) remain to be surmounted. We have mounted a Materials Genome Initiative inspired project that aims to address these challenges by designing, synthesizing, and testing new materials for use in alkaline fuel cells and to discover a set of rules for best practices in the development of future materials for fuel cell applications. In particular, the focus is on anion exchange membrane(AEM) fuel cells, which have advantages over other types of fuel cells in not requiring precious metals and being operable with a variety of fuels at low temperature. The overall strategy of the project employs density-functional theory based first-principles molecular dynamics calculations and dissipative-particle dynamics. In this talk, I will present results from first-principle molecular dynamics component of the proposal, which includes simulations of bulk solutions and idealized confined geometries, both containing cations of interest in the AEM design. Connections to the dissipative-particle dynamics will be made, and comparative results of water structure and distribution, solvation structures and their lifetimes, and hydroxide diffusion constants as functions of temperature, water content, cation spacing, and confinement parameters will be presented. Suggestions of design principles that lead to AEMs with high hydroxide conductivity will be made. Figure 1

Carbonate-Promoted Drift of Alkali Cations in Small Pore Zeolites: Ab Initio Molecular Dynamics Study of CO2 in NaKA Zeolite.

An effect of deblocking of small size (8R, D8R) pores in zeolites due to cation drift is analyzed by using ab initio molecular dynamics (AIMD) at the PBE-D2/PAW level. The effect of carbonate and hydrocarbonate species on the carbon dioxide uptake in NaKA zeolite is demonstrated. It is shown that a hydrocarbonate or carbonate anion can form strong complexes with K+ cation and withdraw it from the 8R window, so that the probability of CO2 diffusion through 8R increases. For the first time, correlations between cationic and HCO3-/CO32- positions are demonstrated in favor of their significant interaction leading to the cationic drift from 8R windows. This phenomenon explains a nonzero CO2 adsorption in narrow pore zeolites upon high Na/K exchange. In a gas mixture, such deblocking effect reduces the separation factor because of the possible passage of both components through the plane of partly open 8R windows.

Hydrogen chloride adsorption on large defective PAHs modeling soot surfaces and influence on water trapping: A DFT and AIMD study

DFT calculations both at 0 K in energy optimization procedure and at finite temperature in ab initio molecular dynamics (AIMD) calculations are used to characterize the adsorption of the hydrogen chloride molecule on a carbonaceous cluster in which a carbon vacancy has been created by removing one carbon atom. This aims at modeling the defective surface of the small graphitic basic structural units that constitute soot nanoparticles, as experimentally evidenced. The results show that HCl can be easily dissociated at the vacancy site of the surface, resulting in the formation of a chlorinated site at the carbonaceous surface, which could have different structures depending on the thermodynamics of the reactions. Then, the resulting chlorinated carbonaceous surfaces are used as model substrates to characterize the first stages of the adsorption of water molecules on chlorinated soot. It is thus shown that adsorbed chlorine atoms may act as an efficient nucleation center for water trapping at the surface of soot. These results represent a new step towards a better understanding of the soot behavior in industrial or domestic fire situations, as well as in marine atmospheric environment where oxidant and chlorinated species are ubiquitous.

Diffusion of a Self-Trapped Hole in a Barium Fluoride Crystal

We present the results of ab initio molecular dynamics (MD) study of a self-trapped hole (Vk-center) in BaF2 crystals. The calculations are performed using the density functional theory in the DFT + U approximation. The configuration of the Vk-center and its possible mechanisms of diffusion throughout the crystal are determined within MD with temperature linearly increasing from 70 to 600 K.

Biopolymeric pH-responsive fluorescent gel for in-vitro and in-vivo colon specific delivery of metronidazole and ciprofloxacin

Biocompatible fluorescent active and pH sensitive gel has been developed using covalently attached riboflavin as proficient fluorophore on crosslinked glycogen. The chemically crosslinked glycogen (cl-Gly/PMAc) has been synthesised by grafting of methacrylic acid (MAc) followed by crosslinking using ethylene glycol dimethacrylate (EGDMA) through free radical polymerization. Afterward, the fluorescent active hydrogel (cl-Gly/PMAc-RB) has been synthesised by post-polymerization modification of cl-Gly/PMAc with riboflavin. The gel properties have been explored by determining rheological parameters. pH responsive swelling and reversible swelling behaviours of cl-Gly/PMAc-RB have been investigated by executing swelling/deswelling/reswelling studies. In-vitro cell cytotoxicity study predicts that the material is non-toxic and biocompatible. cl-Gly/PMAc-RB gel demonstrates excellent release profile towards the release of dual drugs (metronidazole: release ∼ 75% after 24 h and ciprofloxacin: release ∼ 55% after 24 h) in colonic region, which is evidenced from in vitro and in-vivo studies. Finally, ab-initio molecular dynamics study has been carried out to investigate the intricate details of the probable drugs-hydrogel interaction and pH responsive release profile of dual drugs from cl-Gly/PMAc-RB hydrogel in molecular level.

Evolution of local atomic structure during solidification of U116Nb12 liquid: An ab initio molecular dynamics study

By means of ab initio molecular dynamics (AIMD), the evolution of local atomic structures of the U116Nb12 liquid alloy during solidification from 2600 K to 600 K was systemically investigated in terms of the pair correlation function, structure factor, bond angle distribution, coordination number, the Honeycutt-Anderson (HA) and Voronoi index as well as diffusivity and viscosity. The distinctly linear dependence of the mean square displacements (MSDs) as a function of time indicates that the equilibrium configurations are derived from our AIMD simulations. The equations of the volumetric expansion, thermal diffusion and viscosity of the U116Nb12 liquid alloy are presented, respectively. The most abundant structures in the U116Nb12 liquid alloy are those having HA indices of 1551, 1541, 1431, 1441 and 1661. The Voronoi analysis reveals that the distributions of local atomic structures at high temperature are homogeneous, whereas Voronoi polyhedra trend to form <0,2,8,2>, <0,0,12,0>, <0,1,10,2>, <0,1,10,3>, <0,2,8,4>, <0,3,6,5> and <0,3,8,3> with the larger fraction at low temperature. The analysis of chemical short-range order and structural properties suggests that the icosahedra and bcc-type clusters play the dominant roles upon cooling and, the addition of Nb in the U116Nb12 liquid alloy is indeed beneficial to occurrence of the local atomic structural evolution.

Genesis and Stability of Hydronium Ions in Zeolite Channels.

The catalytic sites of acidic zeolite are profoundly altered by the presence of water changing the nature of the Brønsted acid site. High-resolution solid-state NMR spectroscopy shows water interacting with zeolite Brønsted acid sites, converting them to hydrated hydronium ions over a wide range of temperature and thermodynamic activity of water. A signal at 9 ppm was observed at loadings of 2-9 water molecules per Brønsted acid site and is assigned to hydrated hydronium ions on the basis of the evolution of the signal with increasing water content, chemical shift calculations, and the direct comparison with HClO4 in water. The intensity of 1H-29Si cross-polarization signal first increased and then decreased with increasing water chemical potential. This indicates that hydrogen bonds between water molecules and the tetrahedrally coordinated aluminum in the zeolite lattice weaken with the formation of hydronium ion-water clusters and increase the mobility of protons. DFT-based ab initio molecular dynamics studies at multiple temperatures and water concentrations agree well with this interpretation. Above 140 °C, however, fast proton exchange between bridging hydroxyl groups and water occurs even in the presence of only one water molecule per acid site.

Ab Initio Molecular Dynamics Study of Carbonation and Hydrolysis Reactions on Cleaved Quartz (001) Surface

Geochemical trapping (i.e., mineralization) is considered to be the most efficient way for long-term CO2 storage in order to mitigate “global warming effect” induced by anthropogenic CO2 emission. The common view is that the reaction process takes hundreds of years; however, recent field pilots have demonstrated that it only took 2 years to convert injected CO2 to carbonates in reactive basaltic reservoirs. In this work, ab initio molecular dynamics simulations were employed to investigate chemical reactions among CO2, H2O, and newly cleaved quartz (001) surfaces in order to understand the mechanisms of carbonation and hydrolysis reactions, which are essential parts of CO2 mineralization. It is shown that CO2 can react with undercoordinated Si and nonbridging O atoms on the newly cleaved quartz surface, leading to formation of CO3 configuration that is fixed on the surface by Si–O bonds. Furthermore, these Si–O bonds can break under hydrolysis reaction, and HCO3 occurs simultaneously. Electron localizatio...

Reactive and Nonreactive Scattering of HCl from Au(111): An Ab Initio Molecular Dynamics Study.

The HCl + Au(111) system has recently become a benchmark for highly activated dissociative chemisorption, which presumably is strongly affected by electron–hole pair excitation. Previous dynamics calculations, which were based on density functional theory at the generalized gradient approximation level (GGA-DFT) for the molecule–surface interaction, have all overestimated measured reaction probabilities by at least an order of magnitude. Here, we perform ab initio molecular dynamics (AIMD) and AIMD with electronic friction (AIMDEF) calculations employing a density functional that includes the attractive van der Waals interaction. Our calculations model the simultaneous and possibly synergistic effects of surface temperature, surface atom motion, electron–hole pair excitation, the molecular beam conditions of the experiments, and the van der Waals interaction on the reactivity. We find that reaction probabilities computed with AIMDEF and the SRP32-vdW functional still overestimate the measured reaction probabilities, by a factor 18 for the highest incidence energy at which measurements were performed (≈2.5 eV). Even granting that the experiment could have underestimated the sticking probability by about a factor three, this still translates into a considerable overestimation of the reactivity by the current theory. Likewise, scaled transition probabilities for vibrational excitation from ν = 1, j = 1 to ν = 2 are overestimated by the AIMDEF theory, by factors 3–8 depending on the initial conditions modeled. Energy losses to the surface and translational energy losses are, however, in good agreement with experimental values.

Reductive reactions via excess Li in mixture electrolytes of Li ion batteries: an ab initio molecular dynamics study.

The electro-reduction of battery electrolytes plays a critical role in the formation of solid-electrolyte interphase (SEI) layers on the surfaces of negative electrodes. These layers have a significant influence on the performance of rechargeable battery cells. Using ab initio molecular dynamics, we demonstrate the electro-reduction of mixture electrolytes computationally by adding a certain number of excess Li+ first to form the solvation structure and the same number of electrons later for reductive reactions. Our method enables direct observations of the ring opening of one cyclic carbonate followed by merging with another solvent molecule as well as gas generation. When we examined FEC- and EC-based electrolytes, we were able to observe the differences in terms of reaction products. In particular, the two gaseous products that are generated the most are in accordance with recent in situ gas measurements in the literature. The different reaction products of each electrolyte also match well with the SEI constituents reported experimentally. By tracing reaction pathways, we found that Li+ ions facilitate many otherwise difficult electrochemical reactions, presumably by lowering energy barriers. We also found that the excess Li+ forms cationic clusters of Li2PF6+, which enable the reductive decomposition of salt anions and which do not occur easily simply by increasing the electronic occupation. Based on the reaction products of FEC-based electrolytes, here we propose a possible mechanism of polymerization through aldehyde intermediates that are known to bond with surrounding radical anions.